FastQ-Screen issues

Using pigz for parallel gzip operations

2

Hello, it is possible to use pigz for parallel gzip operations? I've allowed 10 threads for fastq_screen, but only a single thread is used for gzip. It would be super...

JoshLoecker

Processing very long reads

2

Devise a way to handle very long reads (e.g. Oxford Nanopore). Maybe make compatible with Minimap2 - as discussed by email with users. Alternatively, break up reads and process with...

StevenWingett

enhancement

priority

rRNA genome

6

Create a rRNA genome for download (--get_genomes)that comprises multiple species and document this in the config file.

StevenWingett

enhancement

Message when passed non-valid path to bowtie2

The message below could be more elegant: (base) ultraviolet@ultraviolet-X555QA:~$ fastq_screen_v0.13.0/fastq_screen fsq_test_dataset.fastq.gz Using fastq_screen v0.13.0 Reading configuration from '/home/ultraviolet/fastq_screen_v0.13.0/fastq_screen.conf' Aligner (--aligner) not specified, but Bowtie2 path and index files found: mapping...

StevenWingett

Could do better

Create a DockerHub container

4

Make FastQ Screen available on DockerHub

StevenWingett

enhancement

good first issue

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code

1

fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code. This seems like a problem since the expected output files are all made, but the reported values...

k1sauce

Could do better

FASTA files

Make FastQ Screen Compatible with FASTA Files

StevenWingett

enhancement

good first issue

Reference genomes on Babraham Bioinformatics website are no longer available for download

1

Running ```shell fastq_screen --get_genomes ``` as instructed [here](https://stevenwingett.github.io/FastQ-Screen/#obtaining-reference-genomes) will return a `404 NOT FOUND` against https://ftp1.babraham.ac.uk/ftpusr46/FastQ_Screen_Genomes/

kuanyili